##fileformat=VCFv4.2
##FILTER=<ID=alignment_artifact,Description="Alignment artifact">
##FILTER=<ID=artifact_in_normal,Description="artifact_in_normal">
##FILTER=<ID=bad_haplotype,Description="Variant near filtered variant on same haplotype.">
##FILTER=<ID=base_quality,Description="alt median base quality">
##FILTER=<ID=chimeric_original_alignment,Description="NuMT variant with too many ALT reads originally from autosome">
##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">
##FILTER=<ID=contamination,Description="contamination">
##FILTER=<ID=duplicate_evidence,Description="evidence for alt allele is overrepresented by apparent duplicates">
##FILTER=<ID=fragment_length,Description="abs(ref - alt) median fragment length">
##FILTER=<ID=germline_risk,Description="Evidence indicates this site is germline, not somatic">
##FILTER=<ID=low_avg_alt_quality,Description="Low average alt quality">
##FILTER=<ID=mapping_quality,Description="ref - alt median mapping quality">
##FILTER=<ID=multiallelic,Description="Site filtered because too many alt alleles pass tumor LOD">
##FILTER=<ID=n_ratio,Description="Ratio of N to alt exceeds specified ratio">
##FILTER=<ID=panel_of_normals,Description="Blacklisted site in panel of normals">
##FILTER=<ID=read_orientation_artifact,Description="orientation bias detected by the orientation bias mixture model">
##FILTER=<ID=read_position,Description="median distance of alt variants from end of reads">
##FILTER=<ID=str_contraction,Description="Site filtered due to contraction of short tandem repeat region">
##FILTER=<ID=strand_artifact,Description="Evidence for alt allele comes from one read direction only">
##FILTER=<ID=strict_strand_bias,Description="Evidence for alt allele is not represented in both directions">
##FILTER=<ID=t_lod,Description="Mutation does not meet likelihood threshold">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MBQ,Number=R,Type=Integer,Description="median base quality">
##FORMAT=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length">
##FORMAT=<ID=MMQ,Number=A,Type=Integer,Description="median mapping quality">
##FORMAT=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read">
##FORMAT=<ID=ORIGINAL_CONTIG_MISMATCH,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig.">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=SA_MAP_AF,Number=3,Type=Float,Description="MAP estimates of allele fraction given z">
##FORMAT=<ID=SA_POST_PROB,Number=3,Type=Float,Description="posterior probabilities of the presence of strand artifact">
##GATKCommandLine=<ID=FilterAlignmentArtifacts,CommandLine="FilterAlignmentArtifacts  --output /home/gmsywss/temp_folder/MCF10A_carboplatin_folder/vcf_folder/mutect2_MCF10A_Carb_Low_cl2_AlignFilt.vcf.gz --bwa-mem-index-image /home/gmsywss/reference_genomes/hs37d5/hs37d5.fa.img --variant /home/gmsywss/temp_folder/MCF10A_carboplatin_folder/vcf_folder/mutect2_MCF10A_Carb_Low_cl2_ALL.vcf.gz --input /home/gmsywss/temp_folder/MCF10A_carboplatin_folder/bam_folder/assembled_haplotype_MCF10A.bam --reference /gpfs/public/reference_genomes/hs37/bwa-mem/hs37d5.fa --tmp-dir /home/gmsywss/temp_folder/scratch_folder  --indel-start-tolerance 5 --fragment-size 1000 --max-failed-realignments 3 --sufficient-good-realignments 2 --dont-skip-filtered-variants false --dont-use-mates false --max-reasonable-fragment-length 100000 --min-aligner-score-difference 20 --num-regular-contigs 25 --minimum-seed-length 14 --drop-ratio 0.2 --seed-split-factor 0.5 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20",Version=4.0.11.0,Date="9 December, 2018 12:24:12 AM SGT">
##GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls  --output /home/gmsywss/temp_folder/MCF10A_carboplatin_folder/vcf_folder/mutect2_MCF10A_Carb_Low_cl2_AlignFilt_FiltMutect.vcf.gz --contamination-table /home/gmsywss/temp_folder/MCF10A_carboplatin_folder/vcf_folder/mutect2_MCF10A_Carb_Low_cl2_contamination.table --variant /home/gmsywss/temp_folder/MCF10A_carboplatin_folder/vcf_folder/mutect2_MCF10A_Carb_Low_cl2_AlignFilt.vcf.gz --tmp-dir /home/gmsywss/temp_folder/scratch_folder  --log-somatic-prior -6.0 --tumor-lod 5.3 --normal-artifact-lod 0.0 --normal-p-value-threshold 0.001 --max-germline-posterior 0.1 --max-alt-allele-count 1 --min-pcr-slippage-size 8 --pcr-slippage-rate 0.1 --pcr-slippage-p-value 0.001 --min-median-mapping-quality 30 --min-median-base-quality 20 --max-median-fragment-length-difference 10000 --min-median-read-position 5 --max-events-in-region 2 --max-strand-artifact-probability 0.99 --min-strand-artifact-allele-fraction 0.01 --contamination-estimate 0.0 --max-contamination-probability 0.1 --unique-alt-read-count 0 --n-ratio Infinity --strict-strand-bias false --orientation-bias-fdr 0.05 --stats Mutect2FilteringStats.tsv --distance-on-haplotype 100 --lod-divided-by-depth 0.005 --non-mt-alts-divided-by-alts 0.85 --mitochondria-mode false --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --correct-overlapping-quality false --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version=4.0.11.0,Date="10 December, 2018 4:05:26 PM SGT">
##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2  --tumor-sample MCF10A_Carb_Low_cl2 --normal-sample MCF10A_DHG11565_HH2GKALXX --germline-resource /home/gmsywss/reference_genomes/hs37d5/GATK_resourceBundle/af-only-gnomad.MUTECT2.b37.vcf.gz --af-of-alleles-not-in-resource 2.5E-6 --bam-output /home/gmsywss/temp_folder/MCF10A_carboplatin_folder/bam_folder/assembled_haplotype_MCF10A.bam --bam-writer-type CALLED_HAPLOTYPES --output /home/gmsywss/temp_folder/MCF10A_carboplatin_folder/vcf_folder/mutect2_MCF10A_Carb_Low_cl2_ALL.vcf.gz --exclude-intervals /home/gmsywss/bedtools2_filters_folder/human_GL000X-NC-decoy.bed --input /home/gmsywss/temp_folder/MCF10A_carboplatin_folder/bam_folder/MCF10A_Carb_Low_cl2_srt_markdup_recal.bam --input /home/gmsywss/temp_folder/MCF10A_carboplatin_folder/bam_folder/MCF10A_DHG11565_HH2GKALXX_srt_merge_markdup_recal.bam --reference /gpfs/public/reference_genomes/hs37/bwa-mem/hs37d5.fa --tmp-dir /home/gmsywss/temp_folder/scratch_folder --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter  --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --initial-pcr-qual 40 --max-population-af 0.01 --downsampling-stride 1 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --max-mnp-distance 1 --ignore-itr-artifacts false --get-af-from-ad false --count-reads false --median-autosomal-coverage 0.0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --correct-overlapping-quality false --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.0.11.0,Date="7 December, 2018 10:09:09 PM SGT">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
##INFO=<ID=IN_PON,Number=0,Type=Flag,Description="site found in panel of normals">
##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal LOD score">
##INFO=<ID=N_ART_LOD,Number=A,Type=Float,Description="log odds of artifact in normal with same allele fraction as tumor">
##INFO=<ID=POP_AF,Number=A,Type=Float,Description="population allele frequencies of alt alleles">
##INFO=<ID=P_CONTAM,Number=1,Type=Float,Description="Posterior probability for alt allele to be due to contamination">
##INFO=<ID=P_GERMLINE,Number=A,Type=Float,Description="Posterior probability for alt allele to be germline variants">
##INFO=<ID=RCNTS,Number=2,Type=Integer,Description="Number of reads passing and failing realignment.">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log odds ratio score for variant">
##MutectVersion=2.1
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
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##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
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##contig=<ID=12,length=133851895>
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##contig=<ID=15,length=102531392>
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##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##contig=<ID=GL000207.1,length=4262>
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##contig=<ID=NC_007605,length=171823>
##contig=<ID=hs37d5,length=35477943>
##filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS.
##normal_sample=MCF10A_DHG11565_HH2GKALXX
##source=FilterAlignmentArtifacts
##source=FilterMutectCalls
##source=Mutect2
##tumor_sample=MCF10A_Carb_Low_cl2
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	MCF10A_Carb_Low_cl2	MCF10A_DHG11565_HH2GKALXX
1	813109	.	A	C	.	PASS	DP=57;ECNT=2;NLOD=8.13;N_ART_LOD=-1.447e+00;POP_AF=0.020;P_CONTAM=5.695e-09;P_GERMLINE=-5.618e+00;RCNTS=1,4;TLOD=19.95	GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:ORIGINAL_CONTIG_MISMATCH:PGT:PID:SA_MAP_AF:SA_POST_PROB	0/1:22,6:0.233:28:10,0:12,6:33,33:263,267:37:43:0:0|1:813109_A_C:0.00,0.212,0.214:0.509,3.349e-03,0.488	0/0:27,0:2.860e-06:27:10,0:17,0:33,0:286,0:0:0:0:0|1:813109_A_C
1	813112	.	T	C	.	PASS	DP=55;ECNT=2;NLOD=8.13;N_ART_LOD=-1.447e+00;POP_AF=0.020;P_CONTAM=5.695e-09;P_GERMLINE=-5.618e+00;RCNTS=1,4;TLOD=19.96	GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:ORIGINAL_CONTIG_MISMATCH:PGT:PID:SA_MAP_AF:SA_POST_PROB	0/1:22,6:0.233:28:10,0:12,6:33,32:263,267:37:40:0:0|1:813109_A_C:0.00,0.212,0.214:0.509,3.349e-03,0.488	0/0:27,0:2.860e-06:27:10,0:17,0:33,0:286,0:0:0:0:0|1:813109_A_C
1	815757	.	G	A	.	PASS	DP=66;ECNT=2;NLOD=9.03;N_ART_LOD=-1.503e+00;POP_AF=0.182;P_CONTAM=2.348e-04;P_GERMLINE=-7.431e+00;RCNTS=2,0;TLOD=10.61	GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:ORIGINAL_CONTIG_MISMATCH:SA_MAP_AF:SA_POST_PROB	0/1:29,5:0.166:34:17,2:12,3:33,34:258,261:37:24:0:0.152,0.00,0.147:4.228e-03,0.300,0.696	0/0:30,0:0.032:30:10,0:20,0:33,0:296,0:0:0:0
1	906904	.	C	A	.	PASS	DP=70;ECNT=1;NLOD=11.09;N_ART_LOD=-1.579e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-1.071e+01;RCNTS=2,0;TLOD=38.81	GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:ORIGINAL_CONTIG_MISMATCH:SA_MAP_AF:SA_POST_PROB	0/1:20,13:0.400:33:5,4:15,9:34,34:258,205:60:30:0:0.364,0.364,0.394:0.043,0.014,0.943	0/0:37,0:2.907e-03:37:19,0:18,0:33,0:285,0:0:0:0
1	1584047	.	C	T	.	PASS	DP=80;ECNT=1;NLOD=5.85;N_ART_LOD=-3.220e-01;POP_AF=0.017;P_CONTAM=1.328e-14;P_GERMLINE=-5.902e+00;RCNTS=0,4;TLOD=22.18	GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:ORIGINAL_CONTIG_MISMATCH:SA_MAP_AF:SA_POST_PROB	0/1:40,9:0.196:49:18,4:22,5:34,34:246,262:57:33:0:0.182,0.00,0.184:6.355e-03,0.148,0.845	0/0:27,1:0.052:28:15,0:12,1:33,34:294,262:21:35:0
1	1821952	.	C	T	.	PASS	DP=47;ECNT=1;NLOD=5.42;N_ART_LOD=-1.279e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-4.727e+00;RCNTS=2,0;TLOD=42.72	GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:ORIGINAL_CONTIG_MISMATCH:SA_MAP_AF:SA_POST_PROB	0/1:15,14:0.490:29:4,3:11,11:34,34:253,254:60:20:0:0.434,0.465,0.483:0.034,0.017,0.949	0/0:18,0:1.803e-04:18:9,0:9,0:33,0:308,0:0:0:0
1	1963733	.	G	A	.	PASS	DP=54;ECNT=1;NLOD=7.82;N_ART_LOD=-1.445e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-7.266e+00;RCNTS=2,1;TLOD=45.77	GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:ORIGINAL_CONTIG_MISMATCH:SA_MAP_AF:SA_POST_PROB	0/1:10,14:0.577:24:5,8:5,6:30,34:260,268:60:30:0:0.556,0.566,0.583:0.027,0.022,0.951	0/0:26,0:0.036:26:10,0:16,0:31,0:279,0:0:0:0
1	2249474	.	G	T	.	PASS	DP=68;ECNT=1;NLOD=8.68;N_ART_LOD=-1.476e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-7.986e+00;RCNTS=2,0;TLOD=64.45	GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:ORIGINAL_CONTIG_MISMATCH:SA_MAP_AF:SA_POST_PROB	0/1:19,20:0.515:39:10,9:9,11:26,34:249,247:60:22:0:0.495,0.485,0.513:0.019,0.027,0.954	0/0:29,0:4.044e-03:29:17,0:12,0:31,0:284,0:0:0:0
1	2545983	.	A	T	.	PASS	DP=65;ECNT=1;NLOD=8.43;N_ART_LOD=-1.462e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-7.886e+00;RCNTS=2,0;TLOD=66.20	GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:ORIGINAL_CONTIG_MISMATCH:SA_MAP_AF:SA_POST_PROB	0/1:15,20:0.568:35:10,8:5,12:34,34:243,251:60:28:0:0.556,0.535,0.571:0.020,0.027,0.953	0/0:28,0:1.683e-04:28:21,0:7,0:34,0:291,0:0:0:0
1	2738084	.	C	A	.	PASS	DP=82;ECNT=1;NLOD=10.49;N_ART_LOD=-1.561e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-1.018e+01;RCNTS=2,0;TLOD=50.85	GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:ORIGINAL_CONTIG_MISMATCH:SA_MAP_AF:SA_POST_PROB	0/1:27,18:0.404:45:13,10:14,8:33,34:259,237:60:22:0:0.384,0.364,0.400:0.017,0.024,0.958	0/0:35,0:0.017:35:20,0:15,0:33,0:313,0:0:0:0
1	2785766	.	G	A	.	PASS	DP=85;ECNT=1;NLOD=10.23;N_ART_LOD=-1.555e+00;POP_AF=2.462e-05;P_CONTAM=0.00;P_GERMLINE=-8.538e+00;RCNTS=2,1;TLOD=73.48	GT:AD:AF:DP:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:ORIGINAL_CONTIG_MISMATCH:SA_MAP_AF:SA_POST_PROB	0/1:24,24:0.502:48:15,13:9,11:34,34:240,243:60:30:0:0.475,0.475,0.500:0.028,0.017,0.955	0/0:34,0:0.028:34:20,0:14,0:33,0:309,0:0:0:0
